Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model

Abstract

BackgroundProstate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases.MethodsIn this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis. We first extracted microRNAs and mRNAs that were differentially expressed between primary PCa and metastatic PCa (MPCa) samples. Then we constructed the MPCa-specific microRNA-mRNA network and screened microRNA biomarkers by a novel bioinformatics model. The model emphasized the characterization of systems stability changes and the network vulnerability with three measurements, i.e. the structurally single-line regulation, the functional importance of microRNA targets and the percentage of transcription factor genes in microRNA unique targets.ResultsWith this model, we identified five microRNAs as putative biomarkers for PCa metastasis. Among them, miR-101-3p and miR-145-5p have been previously reported as biomarkers for PCa metastasis and the remaining three, i.e. miR-204-5p, miR-198 and miR-152, were screened as novel biomarkers for PCa metastasis. The results were further confirmed by the assessment of their predictive power and biological function analysis.ConclusionsFive microRNAs were identified as candidate biomarkers for predicting PCa metastasis based on our network vulnerability analysis model. The prediction performance, literature exploration and functional enrichment analysis convinced our findings. This novel bioinformatics model could be applied to biomarker discovery for other complex diseases.Electronic supplementary materialThe online version of this article (10.1186/s12967-018-1506-7) contains supplementary material, which is available to authorized users.

The role of collagen in cancer: from bench to bedside

“…MiRNAs exert their regulatory activity by affecting a variety of physiological and pathological processes in cancer. Several studies have documented the roles of miRNAs in tumor growth, angiogenesis, and metastasis [89,90], as well as their utility as diagnostic and therapeutic biomarkers [91][92][93]. Regarding the influence of miRNAs on collagen, various miRNAs are regulated in cancer cells to affect distinct functions.…”

Detection of Prostate Cancer Related Genes using Modified Ford-Fulkerson Algorithm in Protein-to-Protein Interaction Network

“…Lin, L. Shen, F. Chen, X. Tang, Z. Sun, C. Du, J. Chen, H. Ding, and B. Shen, [13] predicted the prostate cancer metastasis on the basis of network vulnerability analysis by identifying key microRNAs as biomarkers. The developed system extracted the mRNAs and microRNAs, which were expressed between Metastatic Prostate Cancer (MPCa) samples and primary prostate cancer.…”

Hsa_circ_0000231 knockdown inhibits the glycolysis and progression of colorectal cancer cells by regulating miR-502-5p/MYO6 axis

“…MicroRNAs (miRNAs) are a kind of transcripts of 18-22 nucleotides and work via targeting mRNA 3′-untranslated regions (3′UTR) [8]. MiR-502-5p is indicated to participate in cancer progression [9][10][11]. For example, miR-502-5p overexpression represses cell metastasis in bladder cancer [12].…”